Rooney left Goodison Park for Old Trafford as a teenager in 2004 and went on to score 253 goals for the club, breaking Sir Bobby Charlton's record of 249 earlier this year.
The 31-year-old returns to Merseyside having won the Champions League, five Premier League titles, one FA Cup, three League Cups and the Europa League during his time at United.
Mourinho, a long-time admirer of Rooney even before he took the United job in 2016, wished his club captain well for the future and said he had no choice but to grant his captain's request.
“It is no secret that I have long been an admirer of Wayne; he has been a model professional throughout his time at the club and will remain in the history books for many years to come.
“It is never easy to see a great player playing less football than he would like and I could not stand in his way when he asked to go back to Everton. His experience, focus and determination will be missed and I wish him well for the future.”
Ed Woodward, United's executive vice-chairman, said: “Wayne has been a fantastic servant to United since the moment he signed for us as a prodigiously talented, explosive teenager some 13 seasons ago.
“Who can forget his storybook debut hat trick against Fenerbahce, the spectacular overhead kick against City and the countless match-winning performances in his time here? But after much discussion, the club has decided to accept his request to rejoin his boyhood team.
“He goes having created some of the most magical moments in some of the most successful years in the club's history. Wayne leaves us as our greatest ever goalscorer and having won every major trophy in the game. His record will take decades for anyone to get close to matching and I am extremely grateful for the way he has led from the front since being appointed club captain three years ago.
“On behalf of the whole club and our hundreds of millions of fans around the world, we wish Wayne all the very best for the next phase of his incredible career.”
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies